The Baltic Sea provides a unique model system for studying genetic effects of postglacial colonization and ecological differentiation, because all marine organism must have immigrated after the opening of the Danish Straits 8000 years ago and responded to the development of the steep Skagerrak-Baltic salinity gradient. The red alga Ceramium tenuicorne shows conspicuous variation in growth and reproduction along this gradient. We obtained reproductive data coupled with two types of molecular markers (cox2-3 spacer, mtDNA and random amplified polymorphic DNA, RAPDs). Five mtDNA haplotypes were observed, of which two highly divergent ones were common. One was restricted to and fixed in Oslofjorden, and the other, which was closely related to the three rare haplotypes, was found from southernmost Norway via Kattegat into the Baltic. The RAPD data revealed, on the other hand, a continuous cline corresponsing to the salinity gradient with most of the variation stores at the smallest spatial scale analysed (i.e. within 1 square meter subpopulations). The combined data suggests colonization from a diverse Atlantic gene pool followed by lineage sorting of ancestral mtDNA polymorphisms and strong differential selection among nuclear genotypes along the salinity gradient, including selction for non-recombinant multiplication of those best fit to the marginal low-salinity habitats.